junifer 0.0.4.dev15__tar.gz → 0.0.4.dev22__tar.gz

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev15
+Version: 0.0.4.dev22
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -24,11 +24,33 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE.md
+License-File: AUTHORS.rst
+Requires-Dist: click<8.2,>=8.1.3
+Requires-Dist: numpy<1.27,>=1.24
+Requires-Dist: datalad<0.20,>=0.15.4
+Requires-Dist: pandas<2.2,>=1.4.0
+Requires-Dist: nibabel<5.11,>=3.2.0
+Requires-Dist: nilearn<=0.11.0,>=0.9.0
+Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
+Requires-Dist: ruamel.yaml<0.18,>=0.17
+Requires-Dist: importlib_metadata; python_version < "3.10"
+Requires-Dist: h5py<3.10,>=3.8.0
 Provides-Extra: dev
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
+Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
+Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
+Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
+Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
+Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
+Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
+Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 Provides-Extra: onthefly
-License-File: LICENSE.md
-License-File: AUTHORS.rst
+Requires-Dist: bctpy==0.6.0; extra == "onthefly"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 

junifer-0.0.4.dev22/conda-env.yml

@@ -0,0 +1,33 @@
+name: junifer-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.10,<=3.11
+  - click=8.1.*
+  - numpy>=1.22,<1.27
+  - pandas>=1.4.0,<2.2
+  - nibabel>=3.2.0,<5.2
+  - nilearn>=0.9.0,<=0.10.1
+  - sqlalchemy>=1.4.27,<= 2.0.21
+  - ruamel.yaml=0.17.*
+  - h5py>=3.8,<=3.9
+  - seaborn>=0.11,<=0.13
+  - sphinx>=5.3,<7.3
+  - sphinx-gallery>=0.11.0,<0.15.0
+  - furo>=2022.9.29,<2023.10.0
+  - numpydoc>=1.5.0,<1.6
+  - sphinx-copybutton>=0.5.1,<0.5.3
+  - towncrier>=22.12.0,<23.7
+  - sphinxcontrib-mermaid>=0.8.1,<0.10
+  - tox
+  - ipykernel
+  - pytest-cov
+  - pytest
+  - black
+  - ruff
+  - codespell
+  - pip
+  - pip:
+    - datalad>=0.15.4,<0.20
+    - julearn==0.3.0

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/docs/builtin.rst

@@ -527,7 +527,7 @@ Available
        | NeuroImage, Volume 60, Pages 830-846 (2012).
        | https://doi.org/10.1016/j.neuroimage.2011.11.050.
    * - Areal functional network from Power et al. (2011)
-     - ``Power``
+     - ``Power2011``
      - 0.0.2
      - | Power, J. D., Cohen, A. L., Nelson, S. M. et al.
        | Functional network organization of the human brain.
@@ -540,6 +540,14 @@ Available
        | Prediction of Individual Brain Maturity Using fMRI
        | Science, Volume 329(5997), Pages 1358-1361 (2010).
        | https://doi.org/10.1126/science.1194144
+   * - Areal functional network from Power et al. (2013)
+     - ``Power2013``
+     - 0.0.4
+     - | Power, J. D., Schlaggar, B. L., Lessov-Schlaggar, C. N., &
+       | Petersen, S. E.
+       | Evidence for hubs in human functional brain networks.
+       | Neuron, Volume 79(4), Pages 798–813 (2013).
+       | https://doi.org/10.1016/j.neuron.2013.07.035
 
 
 Planned

junifer-0.0.4.dev22/docs/changes/newsfragments/245.change

@@ -0,0 +1 @@
+Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_

junifer-0.0.4.dev22/docs/changes/newsfragments/245.feature

@@ -0,0 +1 @@
+Add support for ``Power2013`` coordinates by `Synchon Mandal`_

junifer-0.0.4.dev22/docs/changes/newsfragments/253.misc

@@ -0,0 +1 @@
+Update dependencies requirements by `Fede Raimondo`_

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/docs/contribution.rst

@@ -171,7 +171,7 @@ Writing Examples
 The format used for text is reST. Check the `sphinx reST reference`_ for more
 details. The examples are run and displayed in HTML format using
 `sphinx gallery`_. To add an example, just create a ``.py`` file that starts
-either with ``plot_`` or ``run_``, dependending on whether the example generates
+either with ``plot_`` or ``run_``, depending on whether the example generates
 a figure or not.
 
 The first lines of the example should be a Python block comment with a title,

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/docs/installation.rst

@@ -10,14 +10,14 @@ Requirements
 junifer is compatible with `Python`_ >= 3.8 and requires the following packages:
 
 * ``click>=8.1.3,<8.2``
-* ``numpy>=1.22,<1.24``
-* ``datalad>=0.15.4,<0.19``
-* ``pandas>=1.4.0,<1.6``
-* ``nibabel>=3.2.0,<4.1``
-* ``nilearn>=0.9.0,<=0.10.0``
-* ``sqlalchemy>=1.4.27,<= 1.5.0``
+* ``numpy>=1.24,<1.27``
+* ``datalad>=0.15.4,<0.20``
+* ``pandas>=1.4.0,<2.2``
+* ``nibabel>=3.2.0,<5.11``
+* ``nilearn>=0.9.0,<=0.11.0``
+* ``sqlalchemy>=1.4.27,<= 2.1.0``
 * ``ruamel.yaml>=0.17,<0.18``
-* ``h5py>=3.8.0,<3.9``
+* ``h5py>=3.8.0,<3.10``
 
 Depending on the installation method, these packages might be installed
 automatically.

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/ignore_words.txt

@@ -2,3 +2,4 @@ master
 nin
 chang
 sepulcre
+arange

junifer-0.0.4.dev22/junifer/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.0.4.dev22'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev22')

junifer-0.0.4.dev22/junifer/data/VOIs/meta/Power2013_MNI_VOIs.tsv

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{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/junifer/data/coordinates.py

@@ -11,7 +11,7 @@ import numpy as np
 import pandas as pd
 from numpy.typing import ArrayLike
 
-from ..utils.logging import logger, raise_error
+from ..utils.logging import logger, raise_error, warn_with_log
 
 
 # Path to the VOIs
@@ -45,7 +45,9 @@ _available_coordinates: Dict[
     "VigAtt": _vois_meta_path / "VigAtt_VOIs.txt",
     "WM": _vois_meta_path / "WM_VOIs.txt",
     "Power": _vois_meta_path / "Power2011_MNI_VOIs.txt",
+    "Power2011": _vois_meta_path / "Power2011_MNI_VOIs.txt",
     "Dosenbach": _vois_meta_path / "Dosenbach2010_MNI_VOIs.txt",
+    "Power2013": _vois_meta_path / "Power2013_MNI_VOIs.tsv",
 }
 
 
@@ -134,9 +136,27 @@ def load_coordinates(name: str) -> Tuple[ArrayLike, List[str]]:
         The coordinates.
     list of str
         The names of the VOIs.
+
+    Warns
+    -----
+    DeprecationWarning
+        If ``Power`` is provided as the ``name``.
+
     """
     if name not in _available_coordinates:
         raise_error(f"Coordinates {name} not found.")
+
+    # Put up deprecation notice
+    if name == "Power":
+        warn_with_log(
+            msg=(
+                "`Power` has been replaced with `Power2011` and will be "
+                "removed in the next release. For now, it's available for "
+                "backward compatibility."
+            ),
+            category=DeprecationWarning,
+        )
+
     t_coord = _available_coordinates[name]
     if isinstance(t_coord, Path):
         df_coords = pd.read_csv(t_coord, sep="\t", header=None)

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -397,6 +397,10 @@ class JuniferNiftiSpheresMasker(NiftiSpheresMasker):
 
         params = get_params(NiftiSpheresMasker, self)
 
+        # New in nilearn 0.10.1
+        if hasattr(self, "clean_kwargs"):
+            params["clean_kwargs"] = self.clean_kwargs
+
         signals, _ = self._cache(
             _filter_and_extract, ignore=["verbose", "memory", "memory_level"]
         )(

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev15
+Version: 0.0.4.dev22
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -24,11 +24,33 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE.md
+License-File: AUTHORS.rst
+Requires-Dist: click<8.2,>=8.1.3
+Requires-Dist: numpy<1.27,>=1.24
+Requires-Dist: datalad<0.20,>=0.15.4
+Requires-Dist: pandas<2.2,>=1.4.0
+Requires-Dist: nibabel<5.11,>=3.2.0
+Requires-Dist: nilearn<=0.11.0,>=0.9.0
+Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
+Requires-Dist: ruamel.yaml<0.18,>=0.17
+Requires-Dist: importlib_metadata; python_version < "3.10"
+Requires-Dist: h5py<3.10,>=3.8.0
 Provides-Extra: dev
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
+Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
+Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
+Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
+Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
+Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
+Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
+Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 Provides-Extra: onthefly
-License-File: LICENSE.md
-License-File: AUTHORS.rst
+Requires-Dist: bctpy==0.6.0; extra == "onthefly"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/junifer.egg-info/SOURCES.txt

@@ -57,8 +57,11 @@ docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
 docs/changes/newsfragments/233.bugfix
+docs/changes/newsfragments/245.change
+docs/changes/newsfragments/245.feature
 docs/changes/newsfragments/247.doc
 docs/changes/newsfragments/248.change
+docs/changes/newsfragments/253.misc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst
@@ -146,6 +149,7 @@ junifer/data/VOIs/meta/Motor_VOIs.txt
 junifer/data/VOIs/meta/MultiTask_VOIs.txt
 junifer/data/VOIs/meta/PhysioStress_VOIs.txt
 junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt
+junifer/data/VOIs/meta/Power2013_MNI_VOIs.tsv
 junifer/data/VOIs/meta/Rew_VOIs.txt
 junifer/data/VOIs/meta/Somatosensory_VOIs.txt
 junifer/data/VOIs/meta/ToM_VOIs.txt

junifer-0.0.4.dev22/junifer.egg-info/requires.txt

@@ -0,0 +1,30 @@
+click<8.2,>=8.1.3
+numpy<1.27,>=1.24
+datalad<0.20,>=0.15.4
+pandas<2.2,>=1.4.0
+nibabel<5.11,>=3.2.0
+nilearn<=0.11.0,>=0.9.0
+sqlalchemy<=2.1.0,>=1.4.27
+ruamel.yaml<0.18,>=0.17
+h5py<3.10,>=3.8.0
+
+[:python_version < "3.10"]
+importlib_metadata
+
+[dev]
+tox
+pre-commit
+
+[docs]
+seaborn<0.13,>=0.11.2
+sphinx<7.3,>=5.3.0
+sphinx-gallery<0.15.0,>=0.11.0
+furo<2023.10.0,>=2022.9.29
+numpydoc<1.6,>=1.5.0
+julearn<0.4,>=0.3.0
+sphinx-copybutton<0.5.3,>=0.5.1
+towncrier<23.7,>=22.12.0
+sphinxcontrib-mermaid<0.10,>=0.8.1
+
+[onthefly]
+bctpy==0.6.0

{junifer-0.0.4.dev15 → junifer-0.0.4.dev22}/pyproject.toml

@@ -40,15 +40,15 @@ classifiers = [
 ]
 dependencies = [
     "click>=8.1.3,<8.2",
-    "numpy>=1.24,<1.26",
-    "datalad>=0.15.4,<0.19",
-    "pandas>=1.4.0,<1.6",
-    "nibabel>=3.2.0,<4.1",
-    "nilearn>=0.9.0,<=0.10.0",
-    "sqlalchemy>=1.4.27,<= 1.5.0",
+    "numpy>=1.24,<1.27",
+    "datalad>=0.15.4,<0.20",
+    "pandas>=1.4.0,<2.2",
+    "nibabel>=3.2.0,<5.11",
+    "nilearn>=0.9.0,<=0.11.0",
+    "sqlalchemy>=1.4.27,<= 2.1.0",
     "ruamel.yaml>=0.17,<0.18",
     "importlib_metadata; python_version < '3.10'",
-    "h5py>=3.8.0,<3.9",
+    "h5py>=3.8.0,<3.10",
 ]
 dynamic = ["version"]
 
@@ -63,15 +63,15 @@ junifer = "junifer.api.cli:cli"
 [project.optional-dependencies]
 dev = ["tox", "pre-commit"]
 docs = [
-    "seaborn>=0.11.2,<0.12",
-    "Sphinx>=5.3.0,<5.4",
-    "sphinx-gallery>=0.11.0,<0.12",
-    "furo>=2022.9.29,<2023.0.0",
+    "seaborn>=0.11.2,<0.13",
+    "sphinx>=5.3.0,<7.3",
+    "sphinx-gallery>=0.11.0,<0.15.0",
+    "furo>=2022.9.29,<2023.10.0",
     "numpydoc>=1.5.0,<1.6",
-    "julearn==0.3.0",
-    "sphinx-copybutton==0.5.1",
-    "towncrier==22.12.0",
-    "sphinxcontrib-mermaid==0.8.1",
+    "julearn>=0.3.0,<0.4",
+    "sphinx-copybutton>=0.5.1,<0.5.3",
+    "towncrier>=22.12.0,<23.7",
+    "sphinxcontrib-mermaid>=0.8.1,<0.10",
 ]
 onthefly = ["bctpy==0.6.0"]
 

junifer-0.0.4.dev15/conda-env.yml

@@ -1,33 +0,0 @@
-name: junifer-dev
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - python=3.10
-  - click=8.1.*
-  - numpy>=1.22,<1.24
-  - pandas>=1.4.0,<1.6
-  - nibabel>=3.2.0,<4.1
-  - nilearn>=0.9.0,<=0.10.0
-  - sqlalchemy>=1.4.27,<= 1.5.0
-  - ruamel.yaml=0.17.*
-  - h5py=3.8.*
-  - seaborn=0.11.*
-  - Sphinx=5.3.*
-  - sphinx-gallery=0.11.*
-  - furo>=2022.9.29,<2023.0.0
-  - numpydoc=1.5.*
-  - sphinx-copybutton=0.5.*
-  - towncrier=22.12.*
-  - sphinxcontrib-mermaid=0.8.*
-  - tox
-  - ipykernel
-  - pytest-cov
-  - pytest
-  - black
-  - ruff
-  - codespell
-  - pip
-  - pip:
-    - datalad>=0.15.4,<0.19
-    - julearn==0.2.5

junifer-0.0.4.dev15/junifer/_version.py

@@ -1,4 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-__version__ = version = '0.0.4.dev15'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev15')